Admin: Pierre Lindenbaum

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Posts by Pierre Lindenbaum

<prev • 9,236 results • page 2 of 924 • next >
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Answer: A: How to swap the headers between fasta files ?
... * [linearize][1] * use `paste` to get two sequences on the same line. eg. : https://www.biostars.org/p/422316/#422363 * use `cut` to select columns you want * use `tr` to restore the final fasta. [1]: https://gist.github.com/lindenb/2c0d4e11fd8a96d4c345 ...
written 6 days ago by Pierre Lindenbaum128k
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Comment: C: Phasing a trio in multi-sample vcf with zygosity
... so it means that you only need the correct expression for **bcftools view** http://samtools.github.io/bcftools/bcftools.html#expressions or **gatk select variants** https://gatk.broadinstitute.org/hc/en-us/articles/360035891011-JEXL-filtering-expressions . There is no need to convert the genotypes. ...
written 6 days ago by Pierre Lindenbaum128k
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Comment: C: Phasing a trio in multi-sample vcf with zygosity
... > The idea is that in the final annotated file, I can quickly and easily filter each individual by het/hom/ref etc to suit the pattern of inheritance so that's a XYZ problem. What is this pattern of inheritance ? ...
written 7 days ago by Pierre Lindenbaum128k
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Comment: C: Compare columns to find similarities and differences
... I don't understand your problem but you're looking at **awk**. Something like. `awk -F '\t' '{printf("%s\t%s\n",$0,($2==$3 && $1==$4?"TRUE":"FALSE"));}' input.tsv` ...
written 7 days ago by Pierre Lindenbaum128k
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Comment: C: Phasing a trio in multi-sample vcf with zygosity
... > t. However, I'd like to convert the notation to three columns of simply het, hom and ref to make it much easier to analyse. sounds like a [xyz problem][1]. What are you trying to do? [1]: https://en.wikipedia.org/wiki/XY_problem ...
written 8 days ago by Pierre Lindenbaum128k
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Comment: C: Picard CollectSequencingArtifactMetrics error
... it can be any string. You can use the sample name. ...
written 8 days ago by Pierre Lindenbaum128k
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Comment: C: Picard CollectSequencingArtifactMetrics error
... better/faster: cat sample_R1_L001.fastq.gz sample_R1_L002.fastq.gz > sample_R1.fastq.gz bwa can use gzipped fastq files Furthermore, you can parallelize things by mapping each fastq and merge the bam later. ...
written 8 days ago by Pierre Lindenbaum128k
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Comment: C: Picard CollectSequencingArtifactMetrics error
... you should/must have specified some read-groups. https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups ...
written 8 days ago by Pierre Lindenbaum128k
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Answer: C: Picard CollectSequencingArtifactMetrics error
... This error happens when a read is not associated to a read group 1) did you declare the read group in the header `@RG` 2) do you have any read without the `RG` attribute ? ...
written 8 days ago by Pierre Lindenbaum128k
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Comment: C: How To Merge Two Fastq.Gz Files?
... this is wrong. 'Cat' is OK and faster. 'Cat'-ting a set of gzipped files will produce a concatenated gzipped fastq file. ...
written 8 days ago by Pierre Lindenbaum128k

Latest awards to Pierre Lindenbaum

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Choosing Random Set Of Seqs From Larger Set
Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Is there a better tool for visualizing your variants after annotation than Excel
Scholar 3 days ago, created an answer that has been accepted. For A: Parsing a portion of a fasta file header
Scholar 3 days ago, created an answer that has been accepted. For A: quality check of bam files
Good Answer 3 days ago, created an answer that was upvoted at least 5 times. For A: 23Andme Genotype For X Chromosome: Some Have Two Bases, Others Have One
Good Answer 3 days ago, created an answer that was upvoted at least 5 times. For A: Choosing Random Set Of Seqs From Larger Set
Pundit 3 days ago, created a comment with more than 10 votes. For C: I am really pissed off by the bioinformatics software world. Do/can we have a be
Scholar 4 days ago, created an answer that has been accepted. For A: quality check of bam files
Commentator 5 days ago, created a comment with at least 3 up-votes. For C: BWA-MEM read groups usage
Appreciated 10 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 10 days ago, created an answer that has been accepted. For A: quality check of bam files
Scholar 12 days ago, created an answer that has been accepted. For A: quality check of bam files
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Is there a better tool for visualizing your variants after annotation than Excel
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: 23Andme Genotype For X Chromosome: Some Have Two Bases, Others Have One
Appreciated 15 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 16 days ago, created an answer that has been accepted. For A: quality check of bam files
Appreciated 17 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 17 days ago, created an answer that has been accepted. For A: Parsing a portion of a fasta file header
Scholar 19 days ago, created an answer that has been accepted. For A: Parsing a portion of a fasta file header
Scholar 19 days ago, created an answer that has been accepted. For A: Parsing a portion of a fasta file header
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: 23Andme Genotype For X Chromosome: Some Have Two Bases, Others Have One
Scholar 24 days ago, created an answer that has been accepted. For A: Parsing a portion of a fasta file header
Scholar 24 days ago, created an answer that has been accepted. For A: Parsing a portion of a fasta file header
Scholar 25 days ago, created an answer that has been accepted. For A: Parsing a portion of a fasta file header
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: 23Andme Genotype For X Chromosome: Some Have Two Bases, Others Have One

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